Genetic regulatory landscape of gene expression during leaf and stem development in common tobacco

Common tobacco (Nicotiana tabacum L.) is an important allotetraploid crop, yet the genetic regulation of gene expression during development remains poorly understood. Here, we conduct whole-genome and transcriptome sequencing of 220 diverse tobacco accessions to dissect the genetic architecture and regulatory mechanisms underlying trait variation. We identify 3.24 million SNPs and 231,700 InDels, characterizing population structure and genomic features. Our analysis reveals two genetically distinct subpopulations within the flue-cured tobacco that are differentiated across five large genomic segments on chromosomes 2S, 2T, and 12S, which exhibit elevated SNP density, nucleotide diversity, and fixation indices. A genetic regulatory atlas of gene expression, constructed using expression quantitative trait locus (eQTL) mapping across four developmental stages, reveals asymmetric gene expression regulation between subgenomes. Genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) for eight leaf and stem architecture traits identify 43 quantitative trait loci (QTLs) and 153 candidate genes. Furthermore, we jointly analyze TWAS and eQTL summary statistics to construct gene regulatory networks underlying leaf and stem traits, uncovering substantial rewiring of gene regulations across developmental stages. The genomic and transcriptomic datasets generated in this study provide a valuable resource and insights into the genetic architecture of important traits in common tobacco.